Book informationWetware by Dennis BrayPublished by: Yale University PressPrice: £18.99/$28

A BAG of biochemistry less than a millimetre across that spends most of its life attached to pond scum, the single-celled organism Stentor roeselii doesn't sound impressive. Yet its behaviour is remarkably sophisticated. Squirt a jet of water at a Stentor and it will dive into its mucus holdfast, emerging cautiously soon after. But squirt another identical jet at the same Stentor and it ignores it.

How can such complex behaviour arise in such a simple life form? This is the question that Dennis Bray tackles with remarkable clarity and style in this excellent book. In a nutshell, his answer is that living cells, like the single-celled protozoa pictured, are chemical computers. They take information from the environment and process it to produce behavioural "outputs". The processing units are proteins, which perform all the same operations as the logic gates of a computer. Inputs from the environment cause the proteins to flip shape, to aggregate, and to chemically modify other proteins in a cascade of information processing that sweeps through the cell until it reaches effector proteins that make the cell move or change shape.

WORKING through the papers in the black box at Cambridge, Dov Ospovat noticed that as 1856 ended and 1857 began, Darwin’s ideas about species variation began to change. They no longer depended on the natural theological structure of the 1844 essay. Darwin was no longer claiming that variation only ever happened in newly formed and isolated environments where perfect adaptation did not yet apply. Instead, he now claimed that variation could occur at any time, with or without changes in external conditions. It was a complete reversal, and Ospovat was puzzled. There was nothing specific he could point to that might have caused this fundamental change in Darwin’s ideas. It certainly had not come either from Darwin’s study of barnacles or from a weight of collected evidence.’

Quite clear about the huge implications for the development of Darwin’s theory, Ospovat spelled out his discovery. In 1844, Darwin had believed there could be no species variation in nature without a change in geological conditions. He had stated: ‘geological change alone causes adaptation in species’. He was convinced that species could change only when the environment to which they were perfectly adapted changed. Now, he was of the opinion that ‘geological forces are not a causal factor in organic change’.2

In a letter to Hooker in November 1856, only two months after the publication of Wallace’s birds article, Darwin referred to ‘notions’ he was testing that ’species do become changed and that time is a most important element … in such change’.3 Ospovat drew his deductions:

Together, these shifts in emphasis and the numerous others that could be added to the list produced a substantially new conception of the evolu¬tionary process. It is the Darwinian conception we are familiar with from the Origin but it is not a conception that we are justified in reading back into Darwin’s earlier writings.4 ~

What Darwin was suddenly arguing was that variation i? nature was ‘an innate property of organisms’, something natural and unavoidable in all circumstances. Ospovat was absolutely convinced of the importance of this change in Darwin’s thinking.

Everything that Darwin had put at the core of his theory before this point was no longer valid. Suddenly, his new thinking on variation comprised the core of a new theory. Darwin was beginning all over again.

Ospovat was convinced that the mainspring of the theory that led to the Origin less than two years later was understood by Darwin only in the last few months of 1856. He was also convinced that what had turned Darwin’s theory of natural selection into a theory of progressive develop¬ment was his discovery of something he called his ‘principle of divergence’.5 There is, however, nothing in Darwin’s autobiography, in any of his letters, nor anywhere in his journal, to give an account of how or when he was led to or stumbled upon such a principle.

Years after the Origin had been published, when he was celebrated the world over as the greatest naturalist who had ever lived, Darwin described the moment he understood the idea of divergence: ‘I can remember the very spot on the road whilst in my carriage when to my joy the solution occurred to me and this was long after I came to Down’.6 However, of the intellectual process, and of how all his work and experience fused together to illuminate the way ahead, there was not even a hint.

Back in the twentieth century, one researcher had her own reasons for examining the correspondence of Charles Darwin. What she found, or rather did not find, caused her to suspect that things might not have been as open or as transparent between Darwin and Alfred Russel Wallace as everyone had been led to understand.

———————-

Chapter 19 Most unlucky man

BARBARA BEDDALL, newly armed with a master’s degree in zoology from Yale, took exception to Loren Eiseley’s suggestion that Charles Darwin had plagiarised the ideas of Edward Blyth in the development of his theory of evolution. Beddall felt that Eiseley must be misguided, and set out to research Darwin’s original papers and correspondence in Cambridge in an attempt to prove him wrong.

Beddall was unusual. She had taken her first degree in zoology in 1941, but after eight years as a research librarian at Time magazine and seven years as a writer, she returned to zoology and the question of how Darwin had arrived at his ideas. By this time she had gained the reputa¬tion of being a formidable researcher.

Starting at the basics, Beddall began her wider research with a decision to concentrate only on primary source material. She knew from Francis Darwin’s introduction to his father’s letters that there were some gaps in the extant correspondence, but when she began she could have had no idea how crucial those gaps would prove to be. Sifting through the volumi¬nous correspondence, which at that date had not been assembled in date order, Beddall desperately wanted to find the letters exchanged between Wallace and Darwin. They would, she hoped, indicate exactly what Wallace had told Darwin about his own work in that first letter. Instead, she discovered that the letters Darwin had received from Wallace in 1857 and 1858 no longer existed; nor could she find equally important letters from Lyell and Hooker to Darwin in the summer of 1858. Similarly, a vital letter from the American botanist Asa Gray could not be found. I Beddall felt aggrieved. Reporting her lack of success in finding the letters, she said she had not expected such a thing. She had found it ‘very odd’ that the most critical correspondence in Darwin’s files between 1855 and 1858 was missing. She commented: ‘Without these letters, a clear idea of the extent of Wallace’s influence on Darwin is beyond-academic assessment and the full story impossible to gauge’.2 -

Beddall believed Darwin had been much more aware of Wallace than he had ever let on, and that someone had ‘cleaned up the file’.3 In her opinion, Darwin’s son Francis had destroyed the missing letters after his father’s death. The idea that it might have been Darwin himself seems not to have occurred to her.

Although the files might have been purged, there was an intriguing anomaly. Beddall discovered that in the entire Darwin archive, just one small scrap remained of a letter Wallace had written to Darwin. It came from a second letter, which Wallace had written to Darwin in September 1857. Of the first, sent from Macassar in October 1856, there was no trace. The absence of the letters was a great disappointment and Beddall was not convinced by Francis Darwin’s explanation that when files were full, his father discarded old letters to make room for new.4

Darwin had covered his tracks well. He always maintained that he had not received the first letter from Alfred Wallace until the end of April 1857 (rather than inJanuary of the same year).5 However, the timings do not add up. In order to accept Darwin’s assertion, one would have to believe that the most efficient contemporary postal service in the world had taken six months to transfer a letter from the Malay Archipelago to Charles Darwin’s home, rather than the promised two months, without any expla¬nation of where it had been in the meantime. Further, one would have to accept that, due to an extraordinary coincidence, in that lost interval of four months, Charles Darwin conceived of an entirely new species theory and turned away from ideas he had been wedded to for the best part of twenty years. Alternatively, one could theorise that Wallace’s letter had indeed arrived at Darwin’s home at the beginning of the year, and had been in Darwin’s possession during those first four crucial months of 1857, during which his ideas underwent such a dramatic change.

ScienceDaily (June 22, 2009) — Inspired by the behavior of the human eye, Boston College computer scientists have developed a technique that lets computers see objects as fleeting as a butterfly or tropical fish with nearly double the accuracy and 10 times the speed of earlier methods.

The linear solution to one of the most vexing challenges to advancing computer vision has direct applications in the fields of action and object recognition, surveillance, wide-base stereo microscopy and three-dimensional shape reconstruction, according to the researchers, who will report on their advance at the upcoming annual IEEE meeting on computer vision.

BC computer scientists Hao Jiang and Stella X. Yu developed a novel solution of linear algorithms to streamline the computer's work. Previously, computer visualization relied on software that captured the live image then hunted through millions of possible object configurations to find a match. Further compounding the challenge, even more images needed to be searched as objects moved, altering scale and orientation.

Inspired by the behavior of the human eye, Boston College computer scientists have developed a technique that lets computers see objects as fleeting as a butterfly or tropical fish with nearly double the accuracy and 10 times the speed of earlier methods. (Credit: Hao Jiang, Boston College)

Rather than combing through the image bank – a time- and memory-consuming computing task – Jiang and Yu turned to the mechanics of the human eye to give computers better vision.

"When the human eye searches for an object it looks globally for the rough location, size and orientation of the object. Then it zeros in on the details," said Jiang, an assistant professor of computer science. "Our method behaves in a similar fashion, using a linear approximation to explore the search space globally and quickly; then it works to identify the moving object by frequently updating trust search regions."

Molecular Typesetting: How Errors Are Corrected While Proteins Are Being Built

ScienceDaily (June 23, 2009) — Researchers at the Universities of Leeds and Bristol have developed a model of how errors are corrected whilst proteins are being built.

Ensuring that proteins are built correctly is essential to the proper functioning of our bodies, but the ‘quality assurance’ mechanisms that take place during this manufacturing process are not fully understood.“Scientists have been puzzled as to how this process makes so few mistakes”, says Dr Netta Cohen, Reader at the University of Leeds’ School of Computing.To create a protein, the first step involves copying the relevant gene on our DNA onto a template, called RNA. This copying process is carried out by molecular machines called RNA polymerases.

“The RNA polymerase acts like an old fashioned newsprint typesetter, constructing newsprint by assembling letters one at a time. Similarly, RNA polymerase constructs RNA by reading the DNA and adding new letters to the RNA one at a time,” explains Dr Cohen.

There’s no way for the RNA polymerase to ensure that the correct letter is always incorporated at the right spot. “Statistically, we would expect to see a hundred-fold more errors than we actually do, so we know that some error correction must be happening. Otherwise, many more proteins in our bodies would malfunction,” says Dr Cohen.

Biological experiments have shown that the RNA polymerase slides both forwards and backwards along the RNA sequence it has created. What’s more, it has miniature scissors that can then cut out the last few letters of RNA.

So how are errors corrected? Intelligent typesetters would remove the last few letters when they spot an error...

Elephants are the only living representatives of the Proboscidea, a formerly diverse mammalian order whose history began with the 55-million years (mys) old Phosphatherium. Reported here is the discovery from the early late Paleocene of Morocco, ca. 60 mys, of the oldest and most primitive elephant relative, Eritherium azzouzorum n.g., n.sp., which is one of the earliest known representatives of modern placental orders. This well supported stem proboscidean is extraordinarily primitive and condylarth-like. It provides the first dental evidence of a resemblance between the proboscideans and African ungulates (paenungulates) on the one hand and the louisinines and early macroscelideans on the other. Eritherium illustrates the origin of the elephant order at a previously unknown primitive stage among paenungulates and “ungulates.” The primitive morphology of Eritherium suggests a recent and rapid paenungulate radiation after the Cretaceous-Tertiary boundary, probably favoured by early endemic African paleoecosystems. At a broader scale, Eritherium provides a new old calibration point of the placental tree and supports an explosive placental radiation. The Ouled Abdoun basin, which yields the oldest known African placentals, is a key locality for elucidating phylogeny and early evolution of paenungulates and other related endemic African lineages.

Africa-Morocco Afrotheria Paenungulata Placentalia Proboscidea

Footnotes

1To whom correspondence should be addressed. E-mail: gheerbra@mnhn.fr

Author contributions: E.G. designed research, performed research, analyzed data, and wrote the paper.

Microvilli (stereocilia) projecting from the apex of hair cells in the inner ear are actively motile structures that feed energy into the vibration of the inner ear and enhance sensitivity to sound. The biophysical mechanism underlying the hair bundle motor is unknown. In this study, we examined a membrane flexoelectric origin for active movements in stereocilia and conclude that it is likely to be an important contributor to mechanical power output by hair bundles. We formulated a realistic biophysical model of stereocilia incorporating stereocilia dimensions, the known flexoelectric coefficient of lipid membranes, mechanical compliance, and fluid drag. Electrical power enters the stereocilia through displacement sensitive ion channels and, due to the small diameter of stereocilia, is converted to useful mechanical power output by flexoelectricity. This motor augments molecular motors associated with the mechanosensitive apparatus itself that have been described previously. The model reveals stereocilia to be highly efficient and fast flexoelectric motors that capture the energy in the extracellular electro-chemical potential of the inner ear to generate mechanical power output. The power analysis provides an explanation for the correlation between stereocilia height and the tonotopic organization of hearing organs. Further, results suggest that flexoelectricity may be essential to the exquisite sensitivity and frequency selectivity of non-mammalian hearing organs at high auditory frequencies, and may contribute to the “cochlear amplifier” in mammals.

Funding: Financial support was provided by the NIDCD R01 DC04928 & R01 DC06685 (Rabbitt), R01 DC00384 (Brownell), NSF IGERT DGE9987616 and NASA GSRP 56000135 (Breneman). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

* E-mail: r.rabbitt@utah.edu

+++++

Figure 1. Stereocilium flexoelectric biophysics.

a) As an excitatory force is applied the bundle deflects towards the tallest stereocilia and the tip link tension increases. Tip displacement causes the MET to open, current (IT) to enter the stereocilia, thus leading to cable-like membrane depolarization. b–c) Through the membrane flexoelectric effect, depolarization compels a decrease in radius () and increase in height () under constant volume. Changes in length are accompanied by transverse motion due to the staircase gradient in stereocilia lengths and diagonal tip links. Deflections are resisted by actin stiffness and polymerization at the tip, the angular stiffness at the base, and fluid drag in the axial and transverse directions.

Edited by Alec Jeffreys, University of Leicester, Leicester, United Kingdom, and approved May 19, 2009 (received for review March 4, 2009)

Abstract

In general, the strict preservation of broad-scale structure is thought to be critical for maintaining the precisely tuned functionality of vertebrate genomes, although nearly all vertebrate species undergo a small number of programmed local rearrangements during development (e.g., remodeling of adaptive immune receptor loci). However, a limited number of metazoan species undergo much more extensive reorganizations as a normal feature of their development. Here, we show that the sea lamprey (Petromyzon marinus), a jawless vertebrate, undergoes a dramatic remodeling of its genome, resulting in the elimination of hundreds of millions of base pairs (and at least one transcribed locus) from many somatic cell lineages during embryonic development. These studies reveal the highly dynamic nature of the lamprey genome and provide the first example of broad-scale programmed rearrangement of a definitively vertebrate genome. Understanding the mechanisms by which this vertebrate species regulates such extensive remodeling of its genome will provide invaluable insight into factors that can promote stability and change in vertebrate genomes.

The Modern Synthesis (MS) is the current paradigm in evolutionary biology. It was actually built by expanding on the conceptual foundations laid out by its predecessors, Darwinism and neo-Darwinism. For sometime now there has been talk of a new Extended Evolutionary Synthesis (EES), and this article begins to outline why we may need such an extension, and how it may come about. As philosopher Karl Popper has noticed, the current evolutionary theory is a theory of genes, and we still lack a theory of forms. The field began, in fact, as a theory of forms in Darwin’s days, and the major goal that an EES will aim for is a unification of our theories of genes and of forms. This may be achieved through an organic grafting of novel concepts onto the foundational structure of the MS, particularly evolvability, phenotypic plasticity, epigenetic inheritance, complexity theory, and the theory of evolution in highly dimensional adaptive landscapes.

Since the time of the last major conceptual integration in evolutionary biology, the Modern Synthesis of the 1930s and 1940s, the biosciences have made significant advances. The discovery of the DNA, the spread of molecular tools, the rise of high throughput technologies, the pervasive entry of computation, to name but a few, have led to fundamentally different kinds of data and models of biological processes. The theoretical framework of evolutionary biology, by contrast, has remained surprisingly constant over the same period of time. Or so it seems, because upon closer scrutiny it becomes evident that today's evolutionary biology operates with numerous concepts that were not part of the original Synthesis theory. Since their retrospective inclusion into the well defined classical framework is impossible, propositions for a new and expanded theoretical synthesis are on the rise (Carroll 2000; Love 2003; Kutschera and Niklas 2004; Müller 2007; Pigliucci 2007; Rose and Oakley 2007; Carroll 2008; Pigliucci and Müller 2009a). Whatever the specifics of its eventual structure, already now several characteristics by which an Extended Synthesis will reach beyond the confines of the traditional framework can be delineated.

For decades the classical approach has concentrated on population dynamics and speciation. The Modern Synthesis held that populations contain genetic variation caused by random mutation and recombination, and evolution occurs by changes in gene frequencies that are brought about by natural selection, genetic drift, and gene flow. Continued genetic variation results in small changes of quantitative traits, adaptive variants result in differential reproduction, reproductive isolation results in speciation. This theoretical framework has been highly successful in explaining gradual, adaptive, and selectional change in populations. On purpose it excluded modes and phenomena of evolution that did not square with these issues.

The new conceptual input comes from both traditional fields of evolutionary theory and from entirely new areas of evolutionary research. In the traditional fields the understanding of the modes of genetic variation, natural selection, inheritance, and adaptation has undergone considerable modification. Multilevel selection, gene network evolution, epigenetic inheritance, niche inheritance, replicator concepts, among others, provide a more differentiated picture of the variational dynamics of population change. This, in itself, constitutes a major, in parts even iconoclastic theoretical advancement. Even more substantial amendments arise from those fields that address issues not formerly covered by the Synthesis framework, in particular the evolution of organismal complexity. Here belong the factors responsible for the origins of non-adaptive traits, structural innovations, homoplasy, organismal bodyplans, and other phenomena of phenotypic evolution.

Among the new fields, evolutionary developmental biology (EvoDevo) probably has the most far-reaching consequences. EvoDevo has become a highly productive discipline that has diversified into several branches of empirical research. The spectacular discoveries regarding, for instance, gene regulatory evolution, including its deep similarities in organisms that exhibit radically different architectures, have revolutionized our understanding of how development evolves. Less attention has been given to the important ways in which EvoDevo has informed evolutionary theory. Developmental constraint, facilitated variation, epigenetic innovation, dynamical patterning modules, to name but a few of the conceptual innovations provided by EvoDevo, all address problems of phenotypic evolution that were not accessible by the traditional focus on population dynamics. Together with concepts emerging from other new areas of research, such as phenotypic plasticity or evolvability, EvoDevo will contribute key components to any extended evolutionary synthesis.

A characteristic feature of these developments in evolutionary theory is the shift from a population dynamic emphasis favored by the Modern Synthesis towards a causal-mechanistic explanation of phenotypic complexity. The understanding of the evolution of dynamic organizing relations between genes, cells, and tissues, as well as the interactions of these processes with environmental conditions, will permit predictiveness not only about what is adaptively varied but also about what is possible to arise in organismal evolution. The resulting picture of an Extended Synthesis, however preliminary in its present outline, and despite being more advanced in molecular detail, will be less gene centred and more pluralistic than its classical predecessor. An extended framework expands the explanatory reach of evolutionary theory to non-gradual and non-adaptive phenomena of phenotypic evolution and entails a revised understanding of the causal roles of natural selection. More detailed treatments of the conceptual elements shaping the Extended Synthesis can be found in a forthcoming volume (Pigliucci and Müller 2009b).

Despite the costs of mating, females of most taxa mate with multiple males. Polyandrous females are hypothesized to gain genetic benefits for their offspring, but this assumes paternity bias favoring male genotypes that enhance offspring viability. We determined net male genetic effects on female and offspring fitness in a seed beetle and then tested whether fertilization success was biased in favor of high-quality male genotypes in double mating experiments. Contrary to expectations, high-quality male genotypes consistently had a lower postmating fertilization success in two independent assays. Our results imply that sexually antagonistic adaptations have a major and unappreciated influence on male postmating fertilization success. Such genetic variation renders indirect genetic benefits an unlikely driver of the evolution of polyandry.

On June 2, as Congress debated global warming legislation that would raise energy costs to consumers by hundreds of billions of dollars, the Nongovernmental International Panel on Climate Change (NIPCC) released an 880-page book challenging the scientific basis of concerns that global warming is either man-made or would have harmful effects.

In “Climate Change Reconsidered: The 2009 Report of the Nongovernmental International Panel on Climate Change (NIPCC),” coauthors Dr. S. Fred Singer and Dr. Craig Idso and 35 contributors and reviewers present an authoritative and detailed rebuttal of the findings of the United Nations’ Intergovernmental Panel on Climate Change (IPCC), on which the Obama Administration and Democrats in Congress rely for their regulatory proposals.

The scholarship in this book demonstrates overwhelming scientific support for the position that the warming of the twentieth century was moderate and not unprecedented, that its impact on human health and wildlife was positive, and that carbon dioxide probably is not the driving factor behind climate change.

The authors cite thousands of peer-reviewed research papers and books that were ignored by the IPCC, plus additional scientific research that became available after the IPCC’s self-imposed deadline of May 2006.

The Nongovernmental International Panel on Climate Change (NIPCC) is an international panel of nongovernment scientists and scholars who have come together to understand the causes and consequences of climate change. Because it is not a government agency, and because its members are not predisposed to believe climate change is caused by human greenhouse gas emissions, NIPCC is able to offer an independent “second opinion” of the evidence reviewed by the Intergovernmental Panel on Climate Change (IPCC). NIPCC traces its roots to a meeting in Milan in 2003 organized by the Science and Environmental Policy Project (SEPP), a nonprofit research and education organization based in Arlington, Virginia. SEPP, in turn, was founded in 1990 by Dr. S. Fred Singer, an atmospheric physicist, and incorporated in 1992 following Dr. Singer’s retirement from the University of Virginia.

Nature, Not Human Acivity, Rules the Climate: The Summary for Policymakers of the Report of the Nongovernmental International Panel on Climate Change (NIPCC)

This 48-page report by S. Fred Singer and two dozen academic contributors offers a point-by-point rebuttal of many of the most important claims by the Intergovernmental Panel on Climate Change (IPCC). Chapters address attribution, natural cycles, the reliability of climate models, rise of sea-level, ocean heating, the role of carbon dioxide in the atmosphere, and the effects of modest warming.

What should any researcher expect from a journalist beyond the keen intelligence needed to see the newsworthiness of the researcher's work, and the ability to spell his or her name correctly?

For some scientists, the answer is probably 'Not much'. Many tend to think of science journalism as a kind of public-relations service, existing purely to explain new scientific findings to the masses. They may well enjoy reading the results, and give points for a writer's ability to convey the excitement of a discovery, but they will mainly judge an article on its scientific accuracy.

On top of this, some will see science journalism as an ally, useful for shaping the public's understanding of science-related issues such as nuclear proliferation, stem cells or genetically modified crops — and, not incidentally, for making the case for a thriving research enterprise to public and politicians alike.

And a minority, moving beyond perceived self-interest, will point to the deeper value of journalism, which is to cast a fair but sceptical eye over everything in the public sphere — science included. This kind of scrutiny is easy for researchers to applaud when a news report questions dodgy statistics, say, or dubious claims about uncertainties in evolution. It is not so easy when the story takes a critical look at sloppy animal-research practices, overblown claims about climate change or scientists' conflicts of interest. But such examinations are to the benefit of the enterprise as a whole: society needs to see science scrutinized as well as regurgitated if it is to give science its trust, and journalists are an essential part of that process.

At the moment, unfortunately, journalism's future is far from clear. At the 6th World Conference of Science Journalists, which will be held next week in London, and of which Nature is a sponsor, there will probably be many attendees wondering if this is journalism's swan song. Readers — and small ads, once a reliable earner — are migrating to the Internet. New business models in which papers are given away have caused damaging dislocations in some markets, as in Denmark.

Toby Murcott is a writer and broadcaster and former science correspondent for the BBC World Service. A longer version of this Essay will appear in Communicating Biological Sciences, which will be published in November by Ashgate. Email: toby.murcott@ketoe.co.uk.

In the first of three essays, Toby Murcott argues that the process of science needs to be opened up if journalists are to provide proper critique.

There is a rhythm to science news, easy to spot in the mainstream media and as familiar to every science journalist as breathing. It follows the publication cycles of the major peer-reviewed journals such as Science, The Lancet and Nature. As press releases describing research arrive in our inboxes they are scanned for stories, the most newsworthy picked, offered to editors and then reported.

This is not unusual. As British journalist Nick Davies points out in his book Flat Earth News, much of the news agenda in all fields is press-release driven. Journalists are of course trained to stand back and provide a critique, including context and a broader perspective, rather than simply reporting what they read in a press release. But doing so is a particular challenge for science journalists.

To best serve our audiences, we journalists need to be able to see how a new finding fits into the field, know when something new is significant, and have the knowledge and the confidence to ask searching questions. I have a PhD in biochemistry and three years postdoctoral research, so if I am reporting a discovery in my field, I can make a reasonable attempt at understanding the technical detail and will have a sense of the overall history, evolution of ideas and current debates. I will know who is a leader in the field, and who is an outlier; I will be able to distinguish majority views from minority ones. Yet as a science journalist I am expected to cover more than just biochemistry. I need to be able to report on findings in cosmology, ecology, particle physics and much more. To draw on the knowledge of scientists in these fields, I must first find out which scientists are most relevant, and have a sense of their opinions and place within the field. All of this takes time, which reporters often don't have.

Boyce Rensberger was director of the Knight Science Journalism Fellowship programme at the Massachusetts Institute of Technology in Cambridge from 1998 to 2008, and a science reporter for 32 years, chiefly at The Washington Post and The New York Times. Email: boycerensberger@gmail.com

In the second of three essays, Boyce Rensberger tracks the progression of scientific correspondents from cheerleaders to watchdogs.

Science journalism has undergone profound changes since its origin more than a century ago, some more radical than most journalists of today are aware. Although there are legitimate complaints that some current reporters are too close to their sources, or otherwise unable to deliver a disinterested analysis of the field, it is salutary to reflect on how far the profession has come since its beginning.

In the 1890s, there seem to have been no full-time science journalists in either the United States or Britain, although there was one notable part-timer — H. G. Wells. When he wasn't writing science fiction, he penned newspaper articles on genuine scientific findings, arguing that there was a need for writers to translate scientists' jargon and use writing techniques to engage non-specialists. In an 1894 edition of Nature, Wells wrote of the need to employ what today is called narrative non-fiction: "The fundamental principles of construction that underlie such stories as Poe's 'Murders in the Rue Morgue', or Conan Doyle's 'Sherlock Holmes' series, are precisely those that should guide a scientific writer." (See Nature 50, 300–301; 1894.)

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

Abstract

BackgroundMajor transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable. Usually, this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal.

HypothesisI propose that most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on. This biphasic model of evolution incorporates the previously developed concepts of the emergence of protein folds by recombination of small structural units and origin of viruses and cells from a pre-cellular compartmentalized pool of recombining genetic elements. The model is extended to encompass other major transitions. It is proposed that bacterial and archaeal phyla emerged independently from two distinct populations of primordial cells that, originally, possessed leaky membranes, which made the cells prone to rampant gene exchange; and that the eukaryotic supergroups emerged through distinct, secondary endosymbiotic events (as opposed to the primary, mitochondrial endosymbiosis). This biphasic model of evolution is substantially analogous to the scenario of the origin of universes in the eternal inflation version of modern cosmology. Under this model, universes like ours emerge in the infinite multiverse when the eternal process of exponential expansion, known as inflation, ceases in a particular region as a result of false vacuum decay, a first order phase transition process. The result is the nucleation of a new universe, which is traditionally denoted Big Bang, although this scenario is radically different from the Big Bang of the traditional model of an expanding universe. Hence I denote the phase transitions at the end of each inflationary epoch in the history of life Biological Big Bangs (BBB).

Conclusion

A Biological Big Bang (BBB) model is proposed for the major transitions in life's evolution. According to this model, each transition is a BBB such that new classes of biological entities emerge at the end of a rapid phase of evolution (inflation) that is characterized by extensive exchange of genetic information which takes distinct forms for different BBBs. The major types of new forms emerge independently, via a sampling process, from the pool of recombining entities of the preceding generation. This process is envisaged as being qualitatively different from tree-pattern cladogenesis.

ReviewersThis article was reviewed by William Martin, Sergei Maslov, and Leonid Mirny.

Open peer review

This article was reviewed by William Martin, Sergei Maslov, and Leonid Mirny.

quarta-feira, junho 24, 2009

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

Received January 9, 2009; Revised January 30, 2009; Accepted February 4, 2009

ABSTRACT

Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a nonadaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.

Numerous studies over the past 30 years have suggested there is a causal connection between the motion of the Sun through the Galaxy and terrestrial mass extinctions or climate change. Proposed mechanisms include comet impacts (via perturbation of the Oort cloud), cosmic rays and supernovae, the effects of which are modulated by the passage of the Sun through the Galactic midplane or spiral arms. Supposed periodicities in the fossil record, impact cratering dates or climate proxies over the Phanerozoic (past 545 Myr) are frequently cited as evidence in support of these hypotheses. This remains a controversial subject, with many refutations and replies having been published. Here I review both the mechanisms and the evidence for and against the relevance of astronomical phenomena to climate change and evolution. This necessarily includes a critical assessment of time series analysis techniques and hypothesis testing. Some of the studies have suffered from flaws in methodology, in particular drawing incorrect conclusions based on ruling out a null hypothesis. I conclude that there is little evidence for intrinsic periodicities in biodiversity, impact cratering or climate on timescales of tens to hundreds of Myr. Furthermore, Galactic midplane and spiral arm crossings seem to have little or no impact on biological or climate variation above background level. (truncated)

Comments: 51 pages, 7 figures, 140 references. To appear in the International Journal of Astrobiology. For hyperref version with full resolution figures see this http URL